Thanks for reply.
But how then I decide maximum temperature range.Can I go for more then 400K because
beyond this temperature complex get completely denatured.
> you may be better off applying some restraints to the part of the complex
> that you wish to retain. one observation of dissociation in an MD run does
> not mean it's the transition temperature.
>
> On Thu, Jan 13, 2011 at 11:23 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Thanks for reply.
>>
>> Here stablity means I want to keep PROTEIN-DNA complex as such throughout
>> the
>> REMD simulation.When I am heating this complex in MD simulation beyond
>> 363.15K
>> complex getting dissociate.
>>
>> Here I dont want to dissociate complex, I only want to see rondom coil to
>> helix
>> transition.
>>
>> Is it possible at 270 to 363.15K temperature range?
>>
>>
>>
>>
>> > in principle yes, but you need to watch it carefully. it's not clear
>> whether
>> > you are quoting an experiment (hard to know if simulation model
>> reproduces
>> > it, and furthermore what is meant by "stability"- the transition
>> midpoint?
>> > if so, it may still dissociate below that T since it is an ensembler
>> > measurement) or if you quote simulation stability (unlikely that you know
>> > this yet)
>> >
>> >
>> > On Thu, Jan 13, 2011 at 1:30 PM, Sangita Kachhap <sangita.imtech.res.in
>> >wrote:
>> >
>> >>
>> >> Hello all,
>> >>
>> >> I have a protein DNA complex, at the C terminus there is 13 residues
>> random
>> >> coil, I want
>> >> to use here REMD to convert random coil into alpha helix.This complex is
>> >> stable
>> >> at 363.15K, so
>> >> can I use here this temperature 363.15K as maximum temperature to run
>> REMD?
>> >>
>> >> With regard
>> >> Sangita Kachhap
>> >> JRF
>> >> BIC,IMTECH
>> >> CHANDIGARH
>> >>
>> >>
>> >> _______________________________________________
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>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
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>> >
>>
>>
>> With regard
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Jan 17 2011 - 10:30:04 PST
